Mining of single nucleotide polymorphism (SNP) and simple sequence repeats (SSRs) from EST tropical fruits

Authors

  • Rabiatul Adawiah Biotechnology Research Centre, MARDI, P. O. Box 12301, 50774 Kuala Lumpur, Malaysia
  • A.R. Shahril Firdaus Biotechnology Research Centre, MARDI, P. O. Box 12301, 50774 Kuala Lumpur, Malaysia
  • A. Norzihan Biotechnology Research Centre, MARDI, P. O. Box 12301, 50774 Kuala Lumpur, Malaysia
  • A.B. Umi Kalsom Biotechnology Research Centre, MARDI, P. O. Box 12301, 50774 Kuala Lumpur, Malaysia

DOI:

https://doi.org/10.54987/ajpb.v2i2.181

Abstract

The advancement in genomics technology has produced vast amount of expressed sequence
tags (ESTs) sequence from tropical fruits. These resources have increased the public
availability of ESTs sequence from year after year. Therefore, this effort permits mining of
single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) from EST tropical
fruits. SNP and SSR are types of molecular marker which commonly used in modern genetic
analysis for wide application such as diversity analysis, linkage analysis and association study.
In this study, a small scale EST sequences from tropical fruits (pineapple, mango, coconut and
banana) were retrieved from dbEST database (www.ncbi.nlm.nih.gov/dbEST/ ) as of March
2013. Various bioinformatics tools were applied for rapid discovery of SNP and SSR marker
from EST sequences. We analyzed 31,920 unigenes (contigs and singletons) representing a
total of 77,418 ESTs from four tropical fruits for their potential use in developing SNP and SSR
markers. A total of 13,709 EST-SNP were discovered while a total of 4853 EST-SSR were
discovered from these four tropical fruits. The most abundant EST-SSR repeat is from
trinucleotide (15,957 repeats) followed by dinucleotide (13,797 repeats) and tetranucleotide
(973 repeats). Here, 1738 primers from SNP while 2033 primers from SSR were passed
through the setting criteria and were selected for validation using genotyping platform. This
study not only serves as a resource for marker development in tropical fruits but can provide a
better insight into the selection of candidate genes of interest.

Downloads

Published

30.12.2014

How to Cite

Adawiah, R., Shahril Firdaus, A., Norzihan, A., & Kalsom, A. U. (2014). Mining of single nucleotide polymorphism (SNP) and simple sequence repeats (SSRs) from EST tropical fruits. Asian Journal of Plant Biology, 2(2), 48–52. https://doi.org/10.54987/ajpb.v2i2.181

Issue

Vol. 2 No. 2 (2014)

Section

Articles

License

Authors who publish with this journal agree to the following terms:

    1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
    2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
    3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).